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Webinar Tutorial: Using VICE DESeq2 for RNA-seq Differential Expression Analysis

Introduction:

Transcript identification and the quantification of gene expression have been distinct core activities in molecular biology ever since the discovery of RNA’s role as the key intermediate between the genome and the proteome. The power of sequencing RNA lies in the fact that the twin aspects of discovery and quantification can be combined in a single high-throughput sequencing assay called RNA-sequencing (RNA-seq)1

Link to Presentation: https://prezi.com/2oyda-v_oags/?utm_campaign=share&utm_medium=copy

Link to Updated Read the Docs: https://rnaseq-webinar-2019.readthedocs.io/en/latest/

Pre-requisites:

 

 

Test Data for Webinar

Step-by-step guide

Step-1: RMTA Quick Launch

Click on the following button to quick launch an RMTA job in Cyverse DE with test data

https://de.cyverse.org/de/?type=quick-launch&quick-launch-id=21524cbf-6d26-4a62-a8e6-bef731938255&app-id=ed43b8be-daf5-11e9-9393-008cfa5ae621

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Uploading your own data to CyVerse, see Downloading and Uploading Data
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Detailed instruction on using RMTA in either genome-guided or transcriptome-guided can be found on our WIKI: RMTA v2.6.3

Step-2: Rstudio-DESeq2

Here are some helpful notes or resources for anyone performing differential expression.

  • Introduction to differential gene expression analysis using RNA-seq (Written by Friederike Dündar, Luce Skrabanek, Paul Zumbo). Click here
  • Introduction to DGE - click here
  • ANGUS workshop - click here

 

References

  1. A survey of best practices for RNA-seq data analysis. Genome Biol17, 13 (2016). click here